An instance of this class represents a single database definition from the Databases section of mascot.dat. More...

#include <ms_databaseoptions.hpp>

Public Types
enum	{ NUM_THREADS_AUTO_DETECT = -1 }
	Value used to indicate that the number of threads to be used should be automatically determined at runtime. More...

Public Member Functions
	ms_databaseoptions ()
	Default constructor.

	ms_databaseoptions (const ms_databaseoptions &src)
	Copying constructor.

	~ms_databaseoptions ()
	Destructor.

void	copyFrom (const ms_databaseoptions *right)
	Can be used to create a copy of another object.

void	defaultValues ()
	Initialises the instance with default values.

int	getAccessionParseRuleIndex () const
	Returns the value of AccessionParseRuleIndex.

int	getAccessionRefParseRuleIndex () const
	Returns the value of AccessionRefParseRuleIndex.

int	getDBType () const
	Return the database type.

int	getDescriptionParseRuleIndex () const
	Returns the value of DescriptionParseRuleIndex.

std::string	getName () const
	Returns the value of Name.

int	getNumberOfThreads () const
	Returns the value of Threads.

std::string	getPath () const
	Return the value of Path.

const std::string &	getPreceedingComments () const
	Get the comment preceding this database entry.

int	getTaxonomyParseRuleIndex () const
	Returns the value of TaxonomyParseRuleIndex.

bool	isActive () const
	Returns true if the database definition is active and false otherwise.

bool	isLocalRefFile () const
	Returns TRUE if LocalRefFile flag is set to 1 and FALSE otherwise.

bool	isLockMemory () const
	Returns TRUE if MemLock flag is set to 1 and FALSE otherwise.

bool	isMemoryMapFiles () const
	Returns the value of MemMap.

ms_databaseoptions &	operator= (const ms_databaseoptions &right)
	Assignment operator for C++ client applications.

void	setAccessionParseRuleIndex (const int index)
	Change AccessionParseRuleIndex.

void	setAccessionRefParseRuleIndex (const int index)
	Change AccessionRefParseRuleIndex.

void	setActive (const bool value)
	Set the definition as active or inactive.

void	setDBType (const int type)
	Change the database type.

void	setDescriptionParseRuleIndex (const int index)
	Change DescriptionParseRuleIndex.

void	setLocalRefFile (const bool flag)
	Change LocalRefFile.

void	setLockMemory (const bool flag)
	Change MemLock.

void	setMemoryMapFiles (const bool flag)
	Change MemMap.

void	setName (const char *name)
	Change Name.

void	setNumberOfThreads (const int number)
	Change Threads.

void	setPath (const char *path)
	Change Path.

void	setPreceedingComments (const std::string &str)
	Set the comments preceding this database entry.

void	setTaxonomyParseRuleIndex (const int index)
	Change TaxonomyParseRuleIndex.

Detailed Description

An instance of this class represents a single database definition from the Databases section of mascot.dat.

An instance of this class can be normally created within ms_datfile. Before using a definition you must check whether it is active or not (with isActive()). An inactive database definition is allowed to have invalid properties and, therefore, must be ignored for database searches/maintenance. An inactive definition can be made active with setActive(). Before doing so, make sure all the properties are valid.

Instances of the class can be stored in ms_databases.

Member Enumeration Documentation

◆ anonymous enum

anonymous enum

Value used to indicate that the number of threads to be used should be automatically determined at runtime.

See ms_processors::getAutoDetectNumThreads() and getNumberOfThreads().

(Defined as an enum rather than static const int to support VC6)

Enumerator
NUM_THREADS_AUTO_DETECT	Value used to indicate that the number of threads to be used should be automatically determined at runtime.

Member Function Documentation

◆ getAccessionParseRuleIndex()

int getAccessionParseRuleIndex ( ) const

Returns the value of AccessionParseRuleIndex.

Index of the regular expression in the PARSE section that can be used to parse an accession string from a FASTA file title line.

Default is 0.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	Y

Returns: the index for the parse rule.

◆ getAccessionRefParseRuleIndex()

int getAccessionRefParseRuleIndex ( ) const

Returns the value of AccessionRefParseRuleIndex.

Index of the regular expression in the PARSE section that can be used to parse an accession string from a local full text reference file. If there is no local reference file, this value is ignored.

Default is 0.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	Y

Returns: the index for the parse rule.

◆ getDBType()

int getDBType ( ) const

Return the database type.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	Y

Returns: One of the DATABASE_TYPE enumeration values. Note that the returned type is never SLREF.

◆ getDescriptionParseRuleIndex()

int getDescriptionParseRuleIndex ( ) const

Returns the value of DescriptionParseRuleIndex.

Index of the regular expression in the PARSE section that can be used to parse a description string from a FASTA file title line.

Default is 0.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	Y

Returns: the index for the parse rule.

◆ getName()

std::string getName ( ) const

Returns the value of Name.

Each database must have a unique case-sensitive name that is displayed in the search form

The name does not need to be the same as or even similar to the filename of the actual FASTA file.

Do not use spaces, punctuation, or control characters in names.

By default this is empty.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	Y

Returns: the name of the database

Examples: config_mascotdat.cpp.

◆ getNumberOfThreads()

int getNumberOfThreads ( ) const

Returns the value of Threads.

A Mascot search can use multiple threads. If you are running in cluster mode, Threads should be set to 1. Otherwise, specify the same number of threads as processors in your system.

A value of -1 is 'AUTO' which means that the number of threads is set to the maximum possible depending on the number of cores avaiable and the size of the license.

This value has no meaning for spectral libraries

Default, from version 2.6 onwards is -1.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	N

Returns: the number of threads

◆ getPath()

std::string getPath ( ) const

Return the value of Path.

FASTA database files must be on a local disk. Mascot creates its compressed files in the same directory as the original FASTA file. The location of the FASTA file is defined in the Path field. This must be the fully qualified path to the FASTA file, with a wild card in the filename. The delimiters between directories must always be forward slashes, even if Mascot is running on a Windows system.

By default this is empty.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	Y

Returns: the path with wild card

◆ getTaxonomyParseRuleIndex()

int getTaxonomyParseRuleIndex ( ) const

Returns the value of TaxonomyParseRuleIndex.

Index of the taxonomy rule block to be used to parse taxonomy information. If taxonomy information is not available, or is not to be used, this value should be set to 0.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	N

Default is 0.

Returns: Index of the taxonony rule

◆ isActive()

bool isActive ( ) const

Returns true if the database definition is active and false otherwise.

Inactive definitions represent the entries that can be made active by the database manager utility. In the mascot.dat file, they are simply commented out entries.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	Y

Returns: true if the database definition is active

Examples: config_mascotdat.cpp.

◆ isLocalRefFile()

bool isLocalRefFile ( ) const

Returns TRUE if LocalRefFile flag is set to 1 and FALSE otherwise.

Flag to indicate whether a local reference file is available (1) or not (0). For certain databases (MSDB, OWL, and SwissProt), it is possible to have a local reference file, from which full text information can be taken for a Protein View report.

Default is 0.

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	N

Returns: true if the database has a local reference file

◆ isLockMemory()

bool isLockMemory ( ) const

Returns TRUE if MemLock flag is set to 1 and FALSE otherwise.

Flag to indicate whether a memory mapped database file should be locked in memory (1) or not (0).

Default is 0.

See also: isMemoryMapFiles()

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	N

Returns: true if the database should be locked in memory

◆ isMemoryMapFiles()

bool isMemoryMapFiles ( ) const

Returns the value of MemMap.

This flag is to indicate whether the database file should be memory mapped (1) or not (0). Database files should always be memory mapped. Unlike memory locking, this does not consume physical RAM.

Default is 1.

See also: isLockMemory()

Applies to:

Amino acid fasta	Nucleic acid fasta	Spectral library
Y	Y	N

Returns: true if the database is to be memory mapped

◆ setAccessionParseRuleIndex()

void setAccessionParseRuleIndex ( const int index )

Change AccessionParseRuleIndex.

See getAccessionParseRuleIndex() for more information.

Parameters

index is the new value

◆ setAccessionRefParseRuleIndex()

void setAccessionRefParseRuleIndex ( const int index )

Change AccessionRefParseRuleIndex.

See getAccessionRefParseRuleIndex() for more information.

Parameters

index is the new value

◆ setActive()

void setActive ( const bool value )

Set the definition as active or inactive.

See isActive() for more information.

Parameters

value is the new value

◆ setDBType()

void setDBType ( const int type )

Change the database type.

See getDBType() for more information.

Parameters

type	should be one of the DATABASE_TYPE enumeration values. Note that SLREF is not a supported database type for this purpose.

◆ setDescriptionParseRuleIndex()

void setDescriptionParseRuleIndex ( const int index )

Change DescriptionParseRuleIndex.

See getDescriptionParseRuleIndex() for more information.

Parameters

index is the new value

◆ setLocalRefFile()

void setLocalRefFile ( const bool flag )

Change LocalRefFile.

See isLocalRefFile() for more information.

Parameters

flag	is the new value

◆ setLockMemory()

void setLockMemory ( const bool flag )

Change MemLock.

See isLockMemory() for more information.

Parameters

flag	is the new value

◆ setMemoryMapFiles()

void setMemoryMapFiles ( const bool flag )

Change MemMap.

See isMemoryMapFiles() for more information.

Parameters

flag	is the new value

◆ setName()

void setName ( const char * name )

Change Name.

See getName() for more information.

Parameters

name	is the new value

◆ setNumberOfThreads()

void setNumberOfThreads ( const int number )

Change Threads.

See getNumberOfThreads() for more information.

Parameters

number is the new value

◆ setPath()

void setPath ( const char * path )

Change Path.

See getPath() for more information.

Parameters

path	is the new value

◆ setTaxonomyParseRuleIndex()

void setTaxonomyParseRuleIndex ( const int index )

Change TaxonomyParseRuleIndex.

See getTaxonomyParseRuleIndex() for more information.

Parameters

index is the new value

The documentation for this class was generated from the following files:

ms_databaseoptions.hpp
ms_databaseoptions.cpp

Public Types

Public Member Functions

Detailed Description

Member Enumeration Documentation

◆ anonymous enum

Member Function Documentation

◆ getAccessionParseRuleIndex()

◆ getAccessionRefParseRuleIndex()

◆ getDBType()

◆ getDescriptionParseRuleIndex()

◆ getName()

◆ getNumberOfThreads()

◆ getPath()

◆ getTaxonomyParseRuleIndex()

◆ isActive()

◆ isLocalRefFile()

◆ isLockMemory()

◆ isMemoryMapFiles()

◆ setAccessionParseRuleIndex()

◆ setAccessionRefParseRuleIndex()

◆ setActive()

◆ setDBType()

◆ setDescriptionParseRuleIndex()

◆ setLocalRefFile()

◆ setLockMemory()

◆ setMemoryMapFiles()

◆ setName()

◆ setNumberOfThreads()

◆ setPath()

◆ setTaxonomyParseRuleIndex()